Oral Presentation HUPO 2019 - 18th Human Proteome Organization World Congress

Characterization and turnover of RNA-binding proteins: novel insights into ribosome maintenance (#84)

Jakob Trendel 1 2 , Matilde Bertolini 1 3 , Guenter Kramer 1 3 , Bernd Bukau 1 3 , Jeroen Krijgsveld 1 4
  1. German Cancer Research Center (DKFZ), Heidelberg, Germany
  2. European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
  3. Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
  4. Heidelberg University, Medical Faculty, Heidelberg, Germany

To understand the functional interplay of protein and RNA, we have recently developed a methodology to globally identify proteins that interact with RNA, independent of the RNA-biotype. The method, termed XRNAX, purifies protein-RNA complexes, serving as a starting point for detailed exploration of the proteins and RNA they contain. Specifically, we have used this to globally characterize RNA-interactomes in various cell lines, to determine dynamic changes in interaction networks upon cellular stress, and to identify protein-RNA interaction sites. In addition, we used pulsed-SILAC labelling to investigate if binding to RNA influences protein stability. Indeed, we found that in MCF7 cells the half-life of RNA-bound proteins was on average 1.6 fold longer than the same proteins in the overall proteome, and up to 5-fold for individual cases, suggesting that protein stabilization can be a general function of RNA when associating with protein. Likewise, ribosomal proteins are overall stabilized on RNA, however half-lives within the ribosome span more than one order of magnitude, suggesting protein-specific exchange from the complex. To investigate the dynamics of ribosome maintenance and turnover in more detail, we combined pulsed-SILAC labelling with sucrose gradient fractionation to determine half-lives of ribosomal proteins in the 40S, 60S, 80S and polysome fraction, demonstrating profound differences in protein stability between these subunits, especially when translation is inhibited. Collectively these data demonstrate ribosome maintenance by exchange of individual proteins from the ensemble, thereby adding a novel dimension to the classical model describing ribosome production at a defined stoichiometry and destruction by subunit.